Friday, November 22, 2013

Last week our Hydro class visited the Muddy River Restoration Project construction site. This project includes “daylighting” of a previously buried section of the river. These types of projects are happening across the country and they highlight a change in our attitude towards urban water systems. In the old days, we polluted rivers and hid them under the ground. Now we protect, cherish and enjoy them as part of our urban environment. This visit was very interesting to me because, this project has been the subject of a previous Senior Design Capstone class (which helped inform some of the design) and also research (see link to paper below). Here is a picture of Mike Andryuk, a former student and now an engineer with the US Army Corps of Engineers, telling us about the site.

Wednesday, November 6, 2013

I am pleased to announce the publication of our opinion article in PNAS. This paper represents a milestone in our continuing crusade to change modeling of microbial ecology. You know, we used to (and often still do) model microbes as if they are chemical molecules. This approach does not allow us to account for their heterogeneity and it limits how much complexity we can include. Also, and this is the main point of this specific paper, it prohibits us from using any of the individual-based observations (IBOs) generated using novel single-cell observational and experimental techniques. Microbial ecologists are drowning in a flood of IBOs and, just as with systems biology years ago, new analysis tools are needed. Individual-based models (IBMs) to the rescue! This paper lays out our vision for combining IBMs and IBOs, which leads to microbial individual-based ecology (µIBE). Here are links to the paper and a couple of news coverages: